I am receiving the following errors when attempting to perform allelic
crosstalk calibration on a dataset using a custom CDF. I don't know
if this is indicative of errors in the internal structure of the CDF,
or if there are parameters that I must pass to
AllelicCrosstalkCalibration due to the properties of the CDF (i.e. #
of chromosomes, etc.)
> library("aroma.affymetrix")
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3
for help.
R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
R.utils v1.1.3 (2009-01-12) successfully loaded. See ?R.utils for
help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for
help.
Loading required package: R.rsp
R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
Loading required package: digest
Loading required package: aroma.light
aroma.light v1.11.1 (2009-01-12) successfully loaded. See ?aroma.light
for help.
aroma.core v1.0.0 (2009-01-12) successfully loaded. See ?aroma.core
for help.
Loading required package: affxparser
Loading required package: R.huge
R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help.
Loading required package: aroma.apd
aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for
help.
aroma.affymetrix v1.0.0 (2009-01-12) successfully loaded. See ?
aroma.affymetrix for help.
>
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> # Don't display too many decimals.
> options(digits=4)
> chipType="MOUSEDIVm520650"
> cdf<-AffymetrixCdfFile$byChipType("MOUSEDIVm520650")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MOUSEDIVm520650
Filename: MOUSEDIVm520650.CDF
Filesize: 463.91MB
Chip type: MOUSEDIVm520650
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 973990
Cells per unit: 7.08
Number of QC units: 4
> gi<-getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: MOUSEDIVm520650
Tags: DMR20090129
Pathname: annotationData/chipTypes/MOUSEDIVm520650/
MOUSEDIVm520650,DMR20090129.ugp
File size: 4.64MB
RAM: 0.00MB
Chip type: MOUSEDIVm520650
> si<-getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: MOUSEDIVm520650
Tags: DMR20090129
Pathname: annotationData/chipTypes/MOUSEDIVm520650/
MOUSEDIVm520650,DMR20090129.ufl
File size: 3.72MB
RAM: 0.00MB
Chip type: MOUSEDIVm520650
Number of enzymes: 2
> acs<-AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: MOUSEDIVm520650
Tags: DMR20090129
Pathname: annotationData/chipTypes/MOUSEDIVm520650/
MOUSEDIVm520650,DMR20090129.acs
File size: 170.91MB
RAM: 0.00MB
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20090129 12:45:11 CST</
createdOn><platform>Affymetrix</platform><chipType>MOUSEDIVm520650</
chipType>
Chip type: MOUSEDIVm520650
Platform: Affymetrix
> csR<-AffymetrixCelSet$byName("mDIV/testset", cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: testset
Tags:
Path: rawData/mDIV/testset/MOUSEDIVm520650
Platform: Affymetrix
Chip type: MOUSEDIVm520650
Number of arrays: 44
Names: SNP_mDIV_A10-10_081308, SNP_mDIV_A10-201_091708, ...,
SNP_mDIV_A9-9_081308
Time period: 2008-08-13 15:39:47 -- 2008-09-18 00:20:33
Total file size: 2899.65MB
RAM: 0.06MB
There were 50 or more warnings (use warnings() to see the first 50)
> acc<-AllelicCrosstalkCalibration(csR, model="CRMAv2")
> print(acc)
AllelicCrosstalkCalibration:
Data set: testset
Input tags:
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: ACC,ra,-XY
Number of files: 44 (2899.65MB)
Platform: Affymetrix
Chip type: MOUSEDIVm520650
Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200,
subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr
"sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075
0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
Output path: probeData/testset,ACC,ra,-XY/MOUSEDIVm520650
Is done: FALSE
RAM: 0.01MB
> csC<-process(acc, verbose=verbose)
20090130 14:03:43|Calibrating data set for allelic cross talk...
Error in if (any(units < 1)) stop("Argument 'units' contains non-
positive indices.") :
missing value where TRUE/FALSE needed
20090130 14:03:43|Calibrating data set for allelic cross talk...done
> traceback()
13: readCdfCellIndices(pathname, ...)
12: getCellIndicesChunk(getPathname(this), units = unitsChunk, ...,
verbose = verbose)
11: fcn(idxs[ii], ...)
10: lapplyInChunks.numeric(units, function(unitsChunk) {
cdfChunk <- getCellIndicesChunk(getPathname(this), units =
unitsChunk,
..., verbose = verbose)
res <- vector("list", length(unitsChunk))
res[[1]] <- unlist(cdfChunk, use.names = useNames)
res
}, chunkSize = 1e+05, useNames = useNames, verbose = verbose)
9: lapplyInChunks(units, function(unitsChunk) {
cdfChunk <- getCellIndicesChunk(getPathname(this), units =
unitsChunk,
..., verbose = verbose)
res <- vector("list", length(unitsChunk))
res[[1]] <- unlist(cdfChunk, use.names = useNames)
res
}, chunkSize = 1e+05, useNames = useNames, verbose = verbose)
8: getCellIndices.AffymetrixCdfFile(cdf, units = subset, useNames =
FALSE,
unlist = TRUE)
7: getCellIndices(cdf, units = subset, useNames = FALSE, unlist =
TRUE)
6: getSubsetToAvg.AllelicCrosstalkCalibration(this)
5: getSubsetToAvg(this)
4: getParameters.AllelicCrosstalkCalibration(this)
3: getParameters(this)
2: process.AllelicCrosstalkCalibration(acc, verbose = verbose)
1: process(acc, verbose = verbose)
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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traceback(), and 3) to post a complete code example.
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